WebAppMain.installLogger only registers log handlers on a couple of top-level namespaces. Records logged under other names appear e.g. in stderr but not in /log/all.
That is fine for core, but very bad for plugins which do their own logging, as these may be in all sorts of package hierarchies. For example, org.jenkinsci for plugins created from archetype. You can even see this with the SSHD plugin which logs something at startup that is lost from the web UI.
The handler should I think be registered at the namespace root. If there is a need to specifically exclude messages from certain kinds of classes, such as those in an app server hosting Jenkins, then these should be blacklisted (e.g. by skipping just those records whose source class name can be defined in a class loader which is an ancestor of that used to load Jenkins.class).